Supplemental Data.Pdf
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Implications in Parkinson's Disease
Journal of Clinical Medicine Review Lysosomal Ceramide Metabolism Disorders: Implications in Parkinson’s Disease Silvia Paciotti 1,2 , Elisabetta Albi 3 , Lucilla Parnetti 1 and Tommaso Beccari 3,* 1 Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy; [email protected] (S.P.); [email protected] (L.P.) 2 Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy 3 Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti, 06123 Perugia, Italy; [email protected] * Correspondence: [email protected] Received: 29 January 2020; Accepted: 20 February 2020; Published: 21 February 2020 Abstract: Ceramides are a family of bioactive lipids belonging to the class of sphingolipids. Sphingolipidoses are a group of inherited genetic diseases characterized by the unmetabolized sphingolipids and the consequent reduction of ceramide pool in lysosomes. Sphingolipidoses include several disorders as Sandhoff disease, Fabry disease, Gaucher disease, metachromatic leukodystrophy, Krabbe disease, Niemann Pick disease, Farber disease, and GM2 gangliosidosis. In sphingolipidosis, lysosomal lipid storage occurs in both the central nervous system and visceral tissues, and central nervous system pathology is a common hallmark for all of them. Parkinson’s disease, the most common neurodegenerative movement disorder, is characterized by the accumulation and aggregation of misfolded α-synuclein that seem associated to some lysosomal disorders, in particular Gaucher disease. This review provides evidence into the role of ceramide metabolism in the pathophysiology of lysosomes, highlighting the more recent findings on its involvement in Parkinson’s disease. Keywords: ceramide metabolism; Parkinson’s disease; α-synuclein; GBA; GLA; HEX A-B; GALC; ASAH1; SMPD1; ARSA * Correspondence [email protected] 1. -
Entrez Symbols Name Termid Termdesc 117553 Uba3,Ube1c
Entrez Symbols Name TermID TermDesc 117553 Uba3,Ube1c ubiquitin-like modifier activating enzyme 3 GO:0016881 acid-amino acid ligase activity 299002 G2e3,RGD1310263 G2/M-phase specific E3 ubiquitin ligase GO:0016881 acid-amino acid ligase activity 303614 RGD1310067,Smurf2 SMAD specific E3 ubiquitin protein ligase 2 GO:0016881 acid-amino acid ligase activity 308669 Herc2 hect domain and RLD 2 GO:0016881 acid-amino acid ligase activity 309331 Uhrf2 ubiquitin-like with PHD and ring finger domains 2 GO:0016881 acid-amino acid ligase activity 316395 Hecw2 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 GO:0016881 acid-amino acid ligase activity 361866 Hace1 HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1 GO:0016881 acid-amino acid ligase activity 117029 Ccr5,Ckr5,Cmkbr5 chemokine (C-C motif) receptor 5 GO:0003779 actin binding 117538 Waspip,Wip,Wipf1 WAS/WASL interacting protein family, member 1 GO:0003779 actin binding 117557 TM30nm,Tpm3,Tpm5 tropomyosin 3, gamma GO:0003779 actin binding 24779 MGC93554,Slc4a1 solute carrier family 4 (anion exchanger), member 1 GO:0003779 actin binding 24851 Alpha-tm,Tma2,Tmsa,Tpm1 tropomyosin 1, alpha GO:0003779 actin binding 25132 Myo5b,Myr6 myosin Vb GO:0003779 actin binding 25152 Map1a,Mtap1a microtubule-associated protein 1A GO:0003779 actin binding 25230 Add3 adducin 3 (gamma) GO:0003779 actin binding 25386 AQP-2,Aqp2,MGC156502,aquaporin-2aquaporin 2 (collecting duct) GO:0003779 actin binding 25484 MYR5,Myo1e,Myr3 myosin IE GO:0003779 actin binding 25576 14-3-3e1,MGC93547,Ywhah -
Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
Download Download
Supplementary Figure S1. Results of flow cytometry analysis, performed to estimate CD34 positivity, after immunomagnetic separation in two different experiments. As monoclonal antibody for labeling the sample, the fluorescein isothiocyanate (FITC)- conjugated mouse anti-human CD34 MoAb (Mylteni) was used. Briefly, cell samples were incubated in the presence of the indicated MoAbs, at the proper dilution, in PBS containing 5% FCS and 1% Fc receptor (FcR) blocking reagent (Miltenyi) for 30 min at 4 C. Cells were then washed twice, resuspended with PBS and analyzed by a Coulter Epics XL (Coulter Electronics Inc., Hialeah, FL, USA) flow cytometer. only use Non-commercial 1 Supplementary Table S1. Complete list of the datasets used in this study and their sources. GEO Total samples Geo selected GEO accession of used Platform Reference series in series samples samples GSM142565 GSM142566 GSM142567 GSM142568 GSE6146 HG-U133A 14 8 - GSM142569 GSM142571 GSM142572 GSM142574 GSM51391 GSM51392 GSE2666 HG-U133A 36 4 1 GSM51393 GSM51394 only GSM321583 GSE12803 HG-U133A 20 3 GSM321584 2 GSM321585 use Promyelocytes_1 Promyelocytes_2 Promyelocytes_3 Promyelocytes_4 HG-U133A 8 8 3 GSE64282 Promyelocytes_5 Promyelocytes_6 Promyelocytes_7 Promyelocytes_8 Non-commercial 2 Supplementary Table S2. Chromosomal regions up-regulated in CD34+ samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/) -
| Hai Lala at Matalamitaka Huoleht I
|HAI LALA AT MATALAMITAKAUS009816096B2 HUOLEHT I (12 ) United States Patent (10 ) Patent No. : US 9 ,816 , 096 B2 Heintz et al. (45 ) Date of Patent: Nov . 14 , 2017 ( 54 ) METHODS AND COMPOSITIONS FOR 6 , 143 , 566 A 11/ 2000 Heintz et al. TRANSLATIONAL PROFILING AND 6 , 156 , 574 A 12 / 2000 Heintz et al. 6 , 252 , 130 B1 6 / 2001 Federoff MOLECULAR PHENOTYPING 6 , 270, 969 B1 8 / 2001 Hartley et al. 6 , 403 ,374 B1 6 / 2002 Tsien et al. (71 ) Applicant: THE ROCKEFELLER 6 , 410 , 317 B1 6 /2002 Farmer UNIVERSITY , New York , NY (US ) 6 , 441 , 269 B1 8 / 2002 Serafini et al . 6 , 485 , 912 B1 11/ 2002 Heintz et al. @ 6 , 495 , 318 B2 12 / 2002 Harney ( 72 ) Inventors: Nathaniel Heintz , Pelham Manor, NY 6 ,635 ,422 B2 10 / 2003 Keene et al. (US ) ; Paul Greengard , New York , NY 6 , 821, 759 B1 11/ 2004 Heintz et al . (US ) ; Myriam Heiman , New York , NY 7 , 098, 031 B2B2 8 /2006 Choulika et al . (US ) ; Anne Schaefer , New York , NY 7 ,297 ,482 B2 11 /2007 Anderson et al . (US ) ; Joseph P . Doyle , New York , NY 7 , 393 , 632 B2 7 / 2008 Cheo et al. 2003 /0119104 A1 6 /2003 Perkins et al . (US ) ; Joseph D . Dougherty , St. Louis , 2004 / 0023256 A1 2 / 2004 Puglisi et al . MO (US ) 2005 / 0009028 Al 1 /2005 Heintz et al. 2006 /0183147 AL 8 /2006 Meyer - Franke (73 ) Assignee : THE ROCKEFELLER 2011/ 0314565 Al 12 /2011 Heintz et al . UNIVERSITY , New York , NY (US ) FOREIGN PATENT DOCUMENTS ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 EP 1132479 A1 9 / 2001 WO WO -01 / 48480 A1 7 /2001 U . -
Investigation of Candidate Genes and Mechanisms Underlying Obesity
Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between -
Supp Material.Pdf
Simon et al. Supplementary information: Table of contents p.1 Supplementary material and methods p.2-4 • PoIy(I)-poly(C) Treatment • Flow Cytometry and Immunohistochemistry • Western Blotting • Quantitative RT-PCR • Fluorescence In Situ Hybridization • RNA-Seq • Exome capture • Sequencing Supplementary Figures and Tables Suppl. items Description pages Figure 1 Inactivation of Ezh2 affects normal thymocyte development 5 Figure 2 Ezh2 mouse leukemias express cell surface T cell receptor 6 Figure 3 Expression of EZH2 and Hox genes in T-ALL 7 Figure 4 Additional mutation et deletion of chromatin modifiers in T-ALL 8 Figure 5 PRC2 expression and activity in human lymphoproliferative disease 9 Figure 6 PRC2 regulatory network (String analysis) 10 Table 1 Primers and probes for detection of PRC2 genes 11 Table 2 Patient and T-ALL characteristics 12 Table 3 Statistics of RNA and DNA sequencing 13 Table 4 Mutations found in human T-ALLs (see Fig. 3D and Suppl. Fig. 4) 14 Table 5 SNP populations in analyzed human T-ALL samples 15 Table 6 List of altered genes in T-ALL for DAVID analysis 20 Table 7 List of David functional clusters 31 Table 8 List of acquired SNP tested in normal non leukemic DNA 32 1 Simon et al. Supplementary Material and Methods PoIy(I)-poly(C) Treatment. pIpC (GE Healthcare Lifesciences) was dissolved in endotoxin-free D-PBS (Gibco) at a concentration of 2 mg/ml. Mice received four consecutive injections of 150 μg pIpC every other day. The day of the last pIpC injection was designated as day 0 of experiment. -
Anti-HIST1H1E K51ac Antibody
FOR RESEARCH USE ONLY! 02/20 Anti-HIST1H1E K51ac Antibody CATALOG NO.: A2051-100 (100 µl) BACKGROUND DESCRIPTION: Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H1 family. Transcripts from this gene lack poly A tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. Histone H1.4 (Histone H1b) (Histone H1s-4), HIST1H1E, H1F4 ALTERNATE NAMES: ANTIBODY TYPE: Polyclonal HOST/ISOTYPE: Rabbit / IgG IMMUNOGEN: Acetylated peptide sequence targeting residues around Lysine 51 of human Histone H1.4 PURIFICATION: Antigen Affinity purified FORM: Liquid FORMULATION: In 0.01 M PBS, pH 7.4, 50% Glycerol, 0.03% proclin 300 SPECIES REACTIVITY: Human STORAGE CONDITIONS: Store at -20ºC. Avoid freeze / thaw cycles. APPLICATIONS AND USAGE: ICC 1:20-1:200, IF 1:50-1:200 This information is only intended as a guide. The optimal dilutions must be determined by the user Immunocytochemistry analysis of HeLa cells using Anti-HIST1H1E K51ac antibody at dilution of 1:100. Immunofluorescent analysis of HeLa cells (treated with sodium butyrate, 30 mM, 4 hrs) using Anti-HIST1H1E K51ac antibody at dilution of 1:100 and Alexa Fluor 488-conjugated Goat Anti-Rabbit IgG (H+L) as secondary antibody. -
14Q13 Deletions FTNW
14q13 deletions rarechromo.org 14q13 deletions A chromosome 14 deletion means that part of one of the body’s chromosomes (chromosome 14) has been lost or deleted. If the deleted material contains important genes, learning disability, developmental delay and health problems may occur. How serious these problems are depends on how much of the chromosome has been deleted, which genes have been lost and where precisely the deletion is. The features associated with 14q13 deletions vary from person to person, but are likely to include a degree of developmental delay, an unusually small or large head, a raised risk of medical problems and unusual facial features. Genes and chromosomes Our bodies are made up of billions of cells. Most of these cells contain a complete set of thousands of genes that act as instructions, controlling our growth, development and how our bodies work. Inside human cells there is a nucleus where the genes are carried on microscopically small, thread-like structures called chromosomes which are made up p arm p arm of DNA. p arm p arm Chromosomes come in pairs of different sizes and are numbered from largest to smallest, roughly according to their size, from number 1 to number 22. In addition to these so-called autosomal chromosomes there are the sex chromosomes, X and Y. So a human cell has 46 chromosomes: 23 inherited from the mother and 23 inherited from the father, making two sets of 23 chromosomes. A girl has two X chromosomes (XX) while a boy will have one X and one Y chromosome (XY). -
Identification of Novel Chemotherapeutic Strategies For
www.nature.com/scientificreports OPEN Identification of novel chemotherapeutic strategies for metastatic uveal melanoma Received: 17 November 2016 Paolo Fagone1, Rosario Caltabiano2, Andrea Russo3, Gabriella Lupo1, Accepted: 09 February 2017 Carmelina Daniela Anfuso1, Maria Sofia Basile1, Antonio Longo3, Ferdinando Nicoletti1, Published: 17 March 2017 Rocco De Pasquale4, Massimo Libra1 & Michele Reibaldi3 Melanoma of the uveal tract accounts for approximately 5% of all melanomas and represents the most common primary intraocular malignancy. Despite improvements in diagnosis and more effective local therapies for primary cancer, the rate of metastatic death has not changed in the past forty years. In the present study, we made use of bioinformatics to analyze the data obtained from three public available microarray datasets on uveal melanoma in an attempt to identify novel putative chemotherapeutic options for the liver metastatic disease. We have first carried out a meta-analysis of publicly available whole-genome datasets, that included data from 132 patients, comparing metastatic vs. non metastatic uveal melanomas, in order to identify the most relevant genes characterizing the spreading of tumor to the liver. Subsequently, the L1000CDS2 web-based utility was used to predict small molecules and drugs targeting the metastatic uveal melanoma gene signature. The most promising drugs were found to be Cinnarizine, an anti-histaminic drug used for motion sickness, Digitoxigenin, a precursor of cardiac glycosides, and Clofazimine, a fat-soluble iminophenazine used in leprosy. In vitro and in vivo validation studies will be needed to confirm the efficacy of these molecules for the prevention and treatment of metastatic uveal melanoma. Uveal melanoma is the most common primary intraocular cancer, and after the skin, the uveal tract is the second most common location for melanoma1. -
Prediction of Tissue-Specific Cis-Regulatory Sequences: Application to the Ascidian Ciona Intestinalis and the Anterior Neurectoderm Maximilian Häussler
Prediction of tissue-specific cis-regulatory sequences: application to the ascidian Ciona intestinalis and the anterior neurectoderm Maximilian Häussler To cite this version: Maximilian Häussler. Prediction of tissue-specific cis-regulatory sequences: application to the ascidian Ciona intestinalis and the anterior neurectoderm. Cellular Biology. Université Paris Sud - Paris XI, 2009. English. tel-00413501 HAL Id: tel-00413501 https://tel.archives-ouvertes.fr/tel-00413501 Submitted on 4 Sep 2009 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Paris XI Discipline Biologie Cellulaire et Moléculaire École doctorale Gènes, Génomes, Cellules Thèse pour obtenir le grade de Docteur de l'Université Paris XI Soutenance prévu le 15. Juillet 2009 par Maximilian Häussler Prédiction des séquences cis-regulatrices tissu-spéci- fiques: application à l'ascidie Ciona intestinalis et au neurectoderme antérieur Prediction of tissue-specific cis-regulatory sequences: application to the ascidian Ciona intestinalis and the anterior neurectoderm Jury President M. Pierre Capy Rapporteurs: M. Nicolas Pollet M. Sebastian Shimeld Examinateur: M. Elia Stupka Directeur de thèse: M. Jean-Stéphane Joly This thesis can be downloaded from http://hal.archives-ouvertes.fr as a PDF file Summary The detection and annotation of cis-regulatory sequences is a difficult problem. -
Identification of the Molecular Mechanisms Underlying Dilated Cardiomyopathy Via Bioinformatic Analysis of Gene Expression Profiles
EXPERIMENTAL AND THERAPEUTIC MEDICINE 13: 273-279, 2017 Identification of the molecular mechanisms underlying dilated cardiomyopathy via bioinformatic analysis of gene expression profiles HU ZHANG1, ZHUO YU2, JIANCHAO HE1, BAOTONG HUA2 and GUIMING ZHANG1 Departments of 1Cardiaovascular Surgery and 2Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China Received March 26, 2015; Accepted April 21, 2016 DOI: 10.3892/etm.2016.3953 Abstract. In the present study, gene expression profiles of binding protein 3 (IGFBP3)], ‘muscle organ development’ patients with dilated cardiomyopathy (DCM) were re‑analyzed (SMAD7) and ‘regulation of cell migration’ [SMAD7, IGFBP3 with bioinformatics tools to investigate the molecular mecha- and insulin receptor (INSR)]. Notably, signal transducer and nisms underlying DCM. Gene expression dataset GSE3585 activator of transcription 3, SMAD7, INSR, CTGF, exportin 1, was downloaded from Gene Expression Omnibus, which IGFBP3 and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase, included seven heart biopsy samples obtained from patients catalytic subunit alpha were hub nodes with the higher degree with DCM and five healthy controls. Differential analysis was in the PPI network. Therefore, the results of the present study performed using a Limma package in R to screen for differen- suggested that DEGs may alter the biological processes of tially expressed genes (DEGs). Functional enrichment analysis ‘nucleosome formation’, ‘cell adhesion’, ‘skeletal system devel- was subsequently conducted for DEGs using the Database opment’, ‘muscle organ development’ and ‘regulation of cell for Annotation, Visualization and Integration Discovery. A migration’ in the development of DCM. protein‑protein interaction (PPI) network was constructed using information from Search Tool for the Retrieval of Introduction Interacting Genes software.